Lateral Gene Transfer and the Origins of Prokaryotic Groups

Boucher, Yan; Douady, Christophe J.; Papke, R. Thane; Walsh, David A.; Me, Boudreau; Cl, Nesbø; Case, Rebecca J.; Doolittle, W. Ford

doi:10.1146/annurev.genet.37.050503.084247

Cited by 356 publications

(275 citation statements)

References 136 publications

Supporting

Mentioning

260

Contrasting

Unclassified

Order By: Relevance

“…Vestergaard et al (2014) also classified the cas subtypes based on cas-protein occurrences for archaea. Phylogenetic analysis of this study also revealed that many functions of the identified cas proteins could be derived from distantly related genomes, plasmids and phages that was agreed to earlier findings (Nelson et al 1999;Zivanovic et al 2002;Boucher et al 2003;Marraffini and Sontheimer 2009;Chellapandi and Ranjani 2011;Spilman et al 2013). Euryarchaea are more diverse phylogenetically than crenarchaea because of they are generally heterotophic in nature and frequent a wide range of natural environments (Vestergaard et al 2014).…”

Section: Discussionsupporting

confidence: 91%

Knowledge-based discovery for designing CRISPR-CAS systems against invading mobilomes in thermophiles

Chellapandi

Ranjani

2015

Syst Synth Biol

View full text Add to dashboard Cite

Clustered regularly interspaced short palindromic repeats (CRISPRs) are direct features of the prokaryotic genomes involved in resistance to their bacterial viruses and phages. Herein, we have identified CRISPR loci together with CRISPR-associated sequences (CAS) genes to reveal their immunity against genome invaders in the thermophilic archaea and bacteria. Genomic survey of this study implied that genomic distribution of CRISPR-CAS systems was varied from strain to strain, which was determined by the degree of invading mobiloms. Direct repeats found to be equal in some extent in many thermopiles, but their spacers were differed in each strain. Phylogenetic analyses of CAS superfamily revealed that genes cmr, csh, csx11, HD domain, devR were belonged to the subtypes of cas gene family. The members in cas gene family of thermophiles were functionally diverged within closely related genomes and may contribute to develop several defense strategies. Nevertheless, genome dynamics, geological variation and host defense mechanism were contributed to share their molecular functions across the thermophiles. A thermophilic archaean, Thermococcus gammotolerans and thermophilic bacteria, Petrotoga mobilis and Thermotoga lettingae have shown superoperons-like appearance to cluster cas genes, which were typically evolved for their defense pathways. A cmr operon was identified with a specific promoter in a thermophilic archaean, Caldivirga maquilingensis. Overall, we concluded that knowledge-based genomic survey and phylogeny-based functional assignment have suggested for designing a reliable genetic regulatory circuit naturally from CRISPR-CAS systems, acquired defense pathways, to thermophiles in future synthetic biology.

show abstract

Section: Discussionsupporting

confidence: 91%

Knowledge-based discovery for designing CRISPR-CAS systems against invading mobilomes in thermophiles

Chellapandi

Ranjani

2015

Syst Synth Biol

View full text Add to dashboard Cite

show abstract

“…Alternatively, traits that are less conserved will be found in small phylogenetic clades ( Figure 1-trait B). Finally, gene loss, convergent evolution and lateral gene transfer can result in the distribution of many traits across multiple phylogenetic groups (Doolittle, 1999;Snel et al, 2002), leading to random associations between phylogenetic and functional relatedness (Boucher et al, 2003) (Figure 1-trait C).…”

Section: Introductionmentioning

confidence: 99%

Phylogenetic conservatism of functional traits in microorganisms

2012

View full text Add to dashboard Cite

A central question in biology is how biodiversity influences ecosystem functioning. Underlying this is the relationship between organismal phylogeny and the presence of specific functional traits. The relationship is complicated by gene loss and convergent evolution, resulting in the polyphyletic distribution of many traits. In microorganisms, lateral gene transfer can further distort the linkage between phylogeny and the presence of specific functional traits. To identify the phylogenetic conservation of specific traits in microorganisms, we developed a new phylogenetic metricconsenTRAIT-to estimate the clade depth where organisms share a trait. We then analyzed the distribution of 89 functional traits across a broad range of Bacteria and Archaea using genotypic and phenotypic data. A total of 93% of the traits were significantly non-randomly distributed, which suggested that vertical inheritance was generally important for the phylogenetic dispersion of functional traits in microorganisms. Further, traits in microbes were associated with a continuum of trait depths (s D ), ranging from a few deep to many shallow clades (average s D : 0.101-0.0011 rRNA sequence dissimilarity). Next, we demonstrated that the dispersion and the depth of clades that contain a trait is correlated with the trait's complexity. Specifically, complex traits encoded by many genes like photosynthesis and methanogenesis were found in a few deep clusters, whereas the ability to use simple carbon substrates was highly phylogenetically dispersed. On the basis of these results, we propose a framework for predicting the phylogenetic conservatism of functional traits depending on the complexity of the trait. This framework enables predicting how variation in microbial composition may affect microbially-mediated ecosystem processes as well as linking phylogenetic and trait-based patterns of biogeography.

show abstract

“…If phylogenetic conservation is related to genetic complexity as predicted by Martiny et al (2012), then enzyme-positive genotypes should be associated with small clades (Figure 1b) since extracellular enzyme production is commonly encoded by a few genes (see references in Supplementary Tables S1-S3). Alternatively, the traits under investigation may be randomly associated with prokaryotic taxa (Figure 1c), possibly resulting from frequent gene gain/loss, rapid convergent evolution or horizontal gene transfer that obscure vertical inheritance (Doolittle, 1999;Gogarten et al, 2002;Snel et al, 2002;Boucher et al, 2003).…”

Section: Introductionmentioning

confidence: 99%

Microdiversity of extracellular enzyme genes among sequenced prokaryotic genomes

2013

View full text Add to dashboard Cite

Understanding the relationship between prokaryotic traits and phylogeny is important for predicting and modeling ecological processes. Microbial extracellular enzymes have a pivotal role in nutrient cycling and the decomposition of organic matter, yet little is known about the phylogenetic distribution of genes encoding these enzymes. In this study, we analyzed 3058 annotated prokaryotic genomes to determine which taxa have the genetic potential to produce alkaline phosphatase, chitinase and b-N-acetyl-glucosaminidase enzymes. We then evaluated the relationship between the genetic potential for enzyme production and 16S rRNA phylogeny using the consenTRAIT algorithm, which calculated the phylogenetic depth and corresponding 16S rRNA sequence identity of clades of potential enzyme producers. Nearly half (49.2%) of the genomes analyzed were found to be capable of extracellular enzyme production, and these were non-randomly distributed across most prokaryotic phyla. On average, clades of potential enzymeproducing organisms had a maximum phylogenetic depth of 0.008004-0.009780, though individual clades varied broadly in both size and depth. These values correspond to a minimum 16S rRNA sequence identity of 98.04-98.40%. The distribution pattern we found is an indication of microdiversity, the occurrence of ecologically or physiologically distinct populations within phylogenetically related groups. Additionally, we found positive correlations among the genes encoding different extracellular enzymes. Our results suggest that the capacity to produce extracellular enzymes varies at relatively fine-scale phylogenetic resolution. This variation is consistent with other traits that require a small number of genes and provides insight into the relationship between taxonomy and traits that may be useful for predicting ecological function.

show abstract

Lateral Gene Transfer and the Origins of Prokaryotic Groups

Cited by 356 publications

References 136 publications

Knowledge-based discovery for designing CRISPR-CAS systems against invading mobilomes in thermophiles

Knowledge-based discovery for designing CRISPR-CAS systems against invading mobilomes in thermophiles

Phylogenetic conservatism of functional traits in microorganisms

Microdiversity of extracellular enzyme genes among sequenced prokaryotic genomes

Contact Info

Product

Resources

About